diff --git a/README.md b/README.md
index c31520a5fe4330347cd6cd8e91488edb9a3d9447..6648301acec8b331b7e4bef657f839ba725da393 100755
--- a/README.md
+++ b/README.md
@@ -132,6 +132,21 @@ In the [example part of documentation](http://aperrin.pages.pasteur.fr/pipeline_
You can find more information in [PanACoTA documentation](http://aperrin.pages.pasteur.fr/pipeline_annotation/html-doc)!
+
+## On cluster
+
+We provide a singularity image, to help running PanACoTA on a cluster.
+
+First, download the singularity image:
+
+ singularity pull --name panacota.img shub://gem-pasteur/PanACoTA:simple
+
+Then, you can run PanACoTA as previously:
+
+ ./panacota.img -h # to get help on the whole PanACoTA program
+ ./panacota.img <subcommand_name> <arguments_for_subcommand> # to run a module of PanACoTA on your data.
+
+
# <a name="develop"></a> Development
This part is for people who want to work on developing `PanACoTA` package. In the documentation, there is a part dedicated to [developers](http://aperrin.pages.pasteur.fr/pipeline_annotation/html-doc/develop.html).
diff --git a/doc/source/examples.rst b/doc/source/examples.rst
index 5ad7cebc199ad4813d7aabefb5f28197202e86ab..d24dc5736775ea7fca8b1b65a7ecb3c54c0ca1b6 100755
--- a/doc/source/examples.rst
+++ b/doc/source/examples.rst
@@ -1,6 +1,6 @@
-========
-Examples
-========
+====================
+Tutorial on examples
+====================
We provide a folder, ``Examples``, containing genomic sequences (in ``Examples/genomes``).
diff --git a/doc/source/index.rst b/doc/source/index.rst
index 79381a072c4d4e590738857460f11373e1c6f471..730bd37624be8fe94ef3aa29e04643629fe06ca0 100644
--- a/doc/source/index.rst
+++ b/doc/source/index.rst
@@ -14,8 +14,8 @@ XXXXXXXXX
whatis
starting
- usage
examples
+ usage
about
diff --git a/doc/source/starting.rst b/doc/source/starting.rst
index 1bfad9e7049280ee111484be2b57aa60ea23087a..1e121975f54922db04225f3fc96f35f9d198f6c8 100755
--- a/doc/source/starting.rst
+++ b/doc/source/starting.rst
@@ -5,34 +5,9 @@ Starting with PanACoTA
``PanACoTA`` is a Python package, developed in Python 3.6.
-Downloading and updating
-========================
-
-
-You can download ``PanACoTA`` source code by downloading an archive of a given release (zip, tar.gz), or by cloning its github repository. By cloning the github repository, you will then be able to update the code to new versions very easily and quickly. Here is how to clone the repository:
-
-.. code-block:: bash
-
- git clone https://github.com/gem-pasteur/PanACoTA.git
-ve your github login, and password.
-
-This will create a repository called ``PanACoTA``. Go inside this repository (``cd PanACoTA``) to install the software, as described hereafter.
-
-If a new version of ``PanACoTA`` is released, and you want to use it, type the following command to update the source code:
-
-.. code-block:: bash
-
- git pull
-
-Then, you will be able to upgrade to the new version (see :ref:`Upgrade section <upgrade>`).
-
-
-
-Installation: '**./make**' and its options
-========================================================
Dependencies
-------------
+============
``PanACoTA`` is written in **python3**. So, you need python3 (and pip3 for installation) to run it.
@@ -65,6 +40,31 @@ For FastTree, we advise to download C code from `here <http://www.microbesonline
You can then add the output ``FastTreeMP`` to your ``$PATH`` to be able to run it from everywhere.
+Installation:
+=============
+
+Downloading and updating
+------------------------
+
+
+You can get ``PanACoTA`` source code by downloading an archive of a given release (zip, tar.gz), or by cloning its github repository. By cloning the github repository, you will then be able to update the code to new versions very easily and quickly. Here is how to clone the repository:
+
+.. code-block:: bash
+
+ git clone https://github.com/gem-pasteur/PanACoTA.git
+ve your github login, and password.
+
+This will create a repository called ``PanACoTA``. Go inside this repository (``cd PanACoTA``) to install the software, as described hereafter.
+
+If a new version of ``PanACoTA`` is released, and you want to use it, type the following command to update the source code:
+
+.. code-block:: bash
+
+ git pull
+
+Then, you will be able to upgrade to the new version (see :ref:`Upgrade section <upgrade>`).
+
+
.. _installing:
Installing ``PanACoTA``
@@ -116,7 +116,7 @@ If you want to install a new version of ``PanACoTA``:
.. note:: If you have permission issues, and installed the package as root, use ``sudo`` before the second command line (``sudo ./make upgrade``) to upgrade. Or, if you installed the package locally, use ``./make upgrade --user`` to upgrade this local version.
-If you installed it by downloading a zip file, see :ref:`Uninstall it <uninstall>`), and install the new version (by cloning gitlab repository, or downloading the new zip file).
+If you installed it by downloading a zip file, :ref:`Uninstall it <uninstall>`, and install the new version (by cloning gitlab repository, or downloading the new zip file).
Quick run
@@ -143,3 +143,18 @@ Each subcommand has its own options and inputs. To get the list of required argu
PanACoTA <subcommand> -h
+Running with singularity image
+==============================
+
+We provide a singularity image, to help running PanACoTA on a cluster.
+
+First, download the singularity image::
+
+ singularity pull --name panacota.img shub://gem-pasteur/PanACoTA
+
+Then, you can run PanACoTA in the same way as previously, using:
+
+.. code-block:: bash
+
+ ./panacota.img -h # to get help on the whole PanACoTA program
+ ./panacota.img <subcommand_name> <arguments_for_subcommand> # to run a module of PanACoTA on your data.
diff --git a/doc/source/usage.rst b/doc/source/usage.rst
index 5211ec8b9d23066a2e568982d15b5dfe3aa807ec..087b3e0e863a06b14bb09f07203587a58dbdf0d4 100755
--- a/doc/source/usage.rst
+++ b/doc/source/usage.rst
@@ -1,6 +1,6 @@
-==========================
-Running PanACoTA: tutorial
-==========================
+=================================
+Running PanACoTA - help by module
+=================================
``PanACoTA`` contains 6 subcommands, for the different steps: